1. Protein 3-Dimensional Structure and Function
Chapter 4
Protein 3-Dimensional Structure and Function

2. Terminology Conformation – spatial arrangement of atoms in a protein
Native conformation – conformation of functional protein

6. Protein Classification
Simple – composed only of amino acid residues
Conjugated – contain prosthetic groups
(metal ions, co-factors, lipids, carbohydrates)
Example: Hemoglobin – Heme

7. Protein Classification
One polypeptide chain - monomeric protein
More than one - multimeric protein
Homomultimer - one kind of chain
Heteromultimer - two or more different chains
(e.g. Hemoglobin is a heterotetramer. It has two alpha chains and two beta chains.)

8. Protein Classification
Fibrous –
polypeptides arranged in long strands or sheets
water insoluble (lots of hydrophobic AA’s)
strong but flexible
Structural (keratin, collagen)
Globular –
polypeptide chains folded into spherical or globular form
water soluble
contain several types of secondary structure
diverse functions (enzymes, regulatory proteins)

9. catalase
keratin
collagen

10. Protein Function Catalysis – enzymes Structural – keratin
Transport – hemoglobin
Trans-membrane transport – Na+/K+ ATPases
Toxins – rattle snake venom, ricin
Contractile function – actin, myosin
Hormones – insulin
Storage Proteins – seeds and eggs
Defensive proteins – antibodies

11. 4 Levels of Protein Structure

12. Non-covalent forces important in determining protein structure
van der Waals
hydrogen bonds
ionic bonds
hydrophobic interactions

13. 1o Structure Determines 2o, 3o, 4o Structure
Sickle Cell Anemia – single amino acid change in hemoglobin related to disease
Osteoarthritis – single amino acid change in collagen protein causes joint damage

14. Classes of 2o Structure
Alpha helix
B-sheet
Loops and turns

15. Alpha-Helix First proposed by Linus Pauling and Robert Corey in 1951
Identified in keratin by Max Perutz
A ubiquitous component of proteins
Stabilized by H-bonds

16. Alpha-Helix Residues per turn: 3.6 Rise per residue: 1.5 Angstroms
Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms
amino hydrogen H-bonds with carbonyl oxygen located 4 AA’s away forms 13 atom loop
Right handed
helix

17. Alpha-Helix
All H-bonds in the alpha-helix are oriented in the same direction giving the helix a dipole with the N-terminus being positive and the C-terminus being negative

18. Alpha-Helix Side chain groups point outwards from the helix
AA’s with bulky side chains less common in alpha-helix
Glycine and proline destabilizes alpha-helix

19. Amphipathic Alpha-Helices+
One side of the helix (dark) has mostly hydrophobic AA’s
Two amphipathic helices can associate through hydrophobic interactions

20. Beta-Strands and Beta-Sheets
Also first postulated by Pauling and Corey, 1951
Strands may be parallel or antiparallel
Rise per residue:
3.47 Angstroms for antiparallel strands
3.25 Angstroms for parallel strands
Each strand of a beta sheet may be pictured as a helix with two residues per turn

21. Beta-Sheets
Beta-sheets formed from multiple side-by-side beta-strands.
Can be in parallel or anti-parallel configuration
Anti-parallel beta-sheets more stable

22. Beta-Sheets
Side chains point alternately above and below the plane of the beta-sheet
2- to 15 beta-strands/beta-sheet
Each strand made of ~ 6 amino acids

23. Loops and turns Loops Loops usually contain hydrophillic residues.
Found on surfaces of proteins
Connect alpha-helices and beta-sheets
Turns
Loops with < 5 AA’s are called turns
Beta-turns are common

24. Beta-turns allows the peptide chain to reverse direction
carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away
proline and glycine are prevalent in beta turns

25. Protein 3-D structure: 3o and 4o structure and protein folding.

26. 3o Structure third level of protein organization
folding of polypeptide chain causes 2o structures to interact
formation of motifs and domains

27. Proteins with similar 1o structure also have similar 3o structure
tuna GDVAKGKKTFVQKCAQCHTVENGGKHKVGPNLWGLFGRKTGQAEGYSYTDANKSKGIVWN yeast 1 GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVWDE rice GNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTANKMAVIWEE tuna ETLMEYLENPKKYIPGTKMIFAGIKKKGERQDLVAYLKSATS yeast 61 NNMSEYLTNPKKYIPGTKMAFGGLKKEKDRNDLITYLKKACE rice NTLYDYLLNPKKYIPGTKMVFPGLKKPQERADLISYLKEATS

28. Common Motifs

29. Motifs Combine to form Domains
Domains are independent folding units in a 3o structure of a protein
Individual domains have specific function
Parallel twisted sheet
Hydrophobic interactions are the major driving force in folding domains
Alpha/beta barrel

30. Protein family members share common domain structures
lactate dehydrogenase
malate dehydrogenase C O - H 2 C O - H 2 3 C O - H
+ NADH
+ NAD+
+ NADH
+ NAD+

31. 4o Structure
Quaternary structure describes the organization of subunits in a protein with multiple subunits (oligomeric protein)
Can have homo-multimers or hetero-multimers
a2b2
a2bg

32. 4o Structure
Determine molecular weight of native protein by gel permeation chromatography
Determine molecular weight of individual subunits by SDS-PAGE
Can use the information to determine subunit composition
If…….
Native protein – 160,000 daltons and
a-Subunit – 50,000 daltons b-Subunit – 30,000 daltons
Then……
Protein can have a2b2 structure

33. 4o Structure Subunits held together by non-covalent interactions
Oligomeric protein is more stable than disassociated subunits
Active site often made up of AA residues from different subunits
4o and 3o structure is often affected by ligand (substrate or inhibitor) binding. Important in enzyme regulation

34. Protein denaturation Tm
Denaturation – disruption of native conformation
Heat commonly used to denature proteins
Tm = temperature where 50% folded/50% unfolded.
Typical Tm = 40-60oC
Tm for thermophiles >100oC (Taq DNA polymerase)
Chemical denaturants Chaotrophic agents = Urea, KCN detergents = SDS

35. Disulfides Bonds Stabilize native structure
Formed after native conformation achieved
Abundant in secreted proteins but not in intracellular proteins
Protein disulfide isomerase catalyzes reduction of incorrect disulfide linkages